Loading BSWiMS
Results
load("./TADPOLE_BSWIMS_Results.RData")
pander::pander(table(TADPOLE_Conv_TRAIN$status))
pander::pander(table(TADPOLE_Conv_TEST$status))
par(op)
Learning BIC
bConvmBess <- BESS(Surv(TimeToEvent,status)~.,TADPOLE_Conv_TRAIN)
pander::pander(bConvmBess$selectedfeatures)
ADAS13, MMSE, FAQ, APOE4,
ABETA, ST2SV, ST9SV, M_ST34TA,
M_ST38TA, M_ST62TA, M_ST23TS,
M_ST25TS, M_ST34TS, M_ST15SA,
M_ST24SA, M_ST26SA, M_ST31SA,
M_ST30SV, M_ST53SV, RD_ST23TA,
RD_ST129TA, RD_ST35TA, RD_ST43TA,
RD_ST44TA, RD_ST45TA, RD_ST51TA,
RD_ST13TS, RD_ST31TS, RD_ST129TS,
RD_ST44TS, RD_ST47TS, RD_ST52TS,
RD_ST54TS, RD_ST55TS, RD_ST57TS,
RD_ST62TS, RD_ST25SA, RD_ST48SA,
RD_ST52SA, RD_ST55SA, RD_ST57SA,
RD_ST60SA, RD_ST23CV, RD_ST26CV,
RD_ST47CV, RD_ST12SV, RD_ST21SV,
RD_ST53SV and RD_ST66SV
ptestl <- predict(bConvmBess,TADPOLE_Conv_TEST)
cval <- mean(ptestl)
ptestl <- predict(bConvmBess,TADPOLE_Conv_TEST) - cval
boxplot(ptestl~TADPOLE_Conv_TEST$status)

ptestr <- exp(ptestl)
predsurv <- cbind(TADPOLE_Conv_TEST$TimeToEvent,
TADPOLE_Conv_TEST$status,
ptestl,
ptestr)
prSurv <- predictionStats_survival(predsurv,"MCI to AD Conversion")


pander::pander(prSurv$CIRisk)
pander::pander(prSurv$CILp)
pander::pander(prSurv$spearmanCI)
prBin <- predictionStats_binary(cbind(TADPOLE_Conv_TEST$status,ptestl),"MCI to AD Conversion")

pander::pander(prBin$aucs)
pander::pander(prBin$CM.analysis$tab)
| Test + |
47 |
36 |
83 |
| Test - |
15 |
87 |
102 |
| Total |
62 |
123 |
185 |
par(op)
Learning EBIC
bConvmBessE <- BESS_EBIC(Surv(TimeToEvent,status)~.,TADPOLE_Conv_TRAIN)
pander::pander(bConvmBessE$selectedfeatures)
ADAS13, MMSE, FAQ, APOE4,
ABETA, ST2SV, ST9SV, M_ST34TA,
M_ST38TA, M_ST62TA, M_ST23TS,
M_ST25TS, M_ST34TS, M_ST15SA,
M_ST24SA, M_ST26SA, M_ST31SA,
M_ST30SV, M_ST53SV, RD_ST23TA,
RD_ST129TA, RD_ST35TA, RD_ST43TA,
RD_ST44TA, RD_ST45TA, RD_ST51TA,
RD_ST13TS, RD_ST31TS, RD_ST129TS,
RD_ST44TS, RD_ST47TS, RD_ST52TS,
RD_ST54TS, RD_ST55TS, RD_ST57TS,
RD_ST62TS, RD_ST25SA, RD_ST48SA,
RD_ST52SA, RD_ST55SA, RD_ST57SA,
RD_ST60SA, RD_ST23CV, RD_ST26CV,
RD_ST47CV, RD_ST12SV, RD_ST21SV,
RD_ST53SV and RD_ST66SV
ptestl <- predict(bConvmBessE,TADPOLE_Conv_TEST)
cval <- mean(ptestl)
ptestl <- predict(bConvmBessE,TADPOLE_Conv_TEST) - cval
boxplot(ptestl~TADPOLE_Conv_TEST$status)

ptestr <- exp(ptestl)
predsurv <- cbind(TADPOLE_Conv_TEST$TimeToEvent,
TADPOLE_Conv_TEST$status,
ptestl,
ptestr)
prSurv <- predictionStats_survival(predsurv,"MCI to AD Conversion")


pander::pander(prSurv$CIRisk)
pander::pander(prSurv$CILp)
pander::pander(prSurv$spearmanCI)
prBin <- predictionStats_binary(cbind(TADPOLE_Conv_TEST$status,ptestl),"MCI to AD Conversion")

pander::pander(prBin$aucs)
pander::pander(prBin$CM.analysis$tab)
| Test + |
50 |
39 |
89 |
| Test - |
12 |
84 |
96 |
| Total |
62 |
123 |
185 |
par(op)
Learning GS
bConvmBessGS <- BESS_GSECTION(Surv(TimeToEvent,status)~.,TADPOLE_Conv_TRAIN)
1-th iteration s.left:1 s.split:31 s.right:49-th iteration s.left:31
s.split:42 s.right:49-th iteration s.left:42 s.split:46 s.right:49-th
iteration s.left:46 s.split:48 s.right:49
pander::pander(bConvmBessGS$selectedfeatures)
ADAS11, MMSE, RAVLT_immediate,
RAVLT_learning, FAQ, APOE4,
WholeBrain, MidTemp, TAU, PTAU,
ST2SV, ST5SV, M_ST13TA, M_ST14TA,
M_ST24TA, M_ST34TS, M_ST58TS,
M_ST15SA, M_ST39SA, M_ST56SA,
M_ST13CV, M_ST24CV, M_ST40CV,
M_ST58CV, M_ST29SV, M_ST66SV,
RD_ST34TA, RD_ST35TA, RD_ST45TA,
RD_ST51TA, RD_ST58TA, RD_ST13TS,
RD_ST23TS, RD_ST25TS, RD_ST35TS,
RD_ST44TS, RD_ST47TS, RD_ST52TS,
RD_ST55TS, RD_ST62TS, RD_ST13SA,
RD_ST24SA, RD_ST46SA, RD_ST51SA,
RD_ST52SA, RD_ST26CV, RD_ST48CV and
RD_ST65SV
ptestl <- predict(bConvmBessGS,TADPOLE_Conv_TEST)
cval <- mean(ptestl)
ptestl <- predict(bConvmBessGS,TADPOLE_Conv_TEST) - cval
boxplot(ptestl~TADPOLE_Conv_TEST$status)

ptestr <- exp(ptestl)
predsurv <- cbind(TADPOLE_Conv_TEST$TimeToEvent,
TADPOLE_Conv_TEST$status,
ptestl,
ptestr)
prSurv <- predictionStats_survival(predsurv,"MCI to AD Conversion")


pander::pander(prSurv$CIRisk)
pander::pander(prSurv$CILp)
pander::pander(prSurv$spearmanCI)
prBin <- predictionStats_binary(cbind(TADPOLE_Conv_TEST$status,ptestl),"MCI to AD Conversion")
